Influenza A virus (IAV) is a major threat to human health with seasonal epidemics, occasional pandemics and emergence of new highly pathogenic strains from the animal reservoir. Our laboratory has shown that the human Annexin A6 (AnxA6) interacts with the IAV M2 proton channel and limits production of progeny IAV from infected cells. We have found that overexpression of AnxA6 impairs morphogenesis and release of progeny viruses. These findings are supported by another study showing that AnxA6 has a critical role in the late endosomal cholesterol balance and affects IAV replication and propagation in AnxA6-overexpressing cells. However, the molecular mechanism responsible for restriction of IAV morphogenesis by AnxA6 is still unclear. AnxA6 is a calcium-dependent phospholipid-binding protein which plays a major role in cellular events such as regulation of cholesterol homeostasis and membrane organisation or repair. AnxA6 is also implicated in the regulation of intracellular signalling pathways required for IAV infection. In this study, we used a combination of virology, cellular biology and biochemistry approaches to decipher the restriction mechanism of IAV by human AnxA6. We found that AnxA6 down-regulates M2 viral protein expression and impairs viral morphogenesis and budding. We also found that AnxA6 regulates chemokines and cytokines expression during viral infection, suggesting that AnxA6 triggers an innate immune response to IAV by modulating signalling pathways required for viral replication. Finally, we observed that IAV down-regulates AnxA6 expression at mRNA level during early stages of infection and at protein level during late infection, suggesting that IAV has developed a strategy to respond to AnxA6 restriction mechanism during viral infection. We conclude that it is essential to better understand the interaction between human AnxA6 and IAV to elucidate the potential of AnxA6 as an antiviral candidate.

Seasonal and pandemic Influenza virus infections cause about three to five million cases of severe illness and about 250,000 to 500,000 deaths world-wide annually according to the WHO. Although investigated intensively, Influenza virus pathogenesis is still not very well understood and hard to predict. Influenza A viruses contain a segmented, single-(-) stranded RNA genome encoding at least 10 different proteins and are highly diverse due to hypermutation and reassortment. In previous work, 56 viral genes from six different influenza A virus isolates had been cloned and genome-wide screened for virus-host protein interactions using yeast-two hybrid technology and several human and chicken cDNA libraries, leading to the identification of 127 high-confidence cellular interactors of which 40 have also been identified by RNA interference in other studies. In this thesis, two of the cellular interactors identified which both bound to the viral multifunctional protein NS1, TRBP and PACT, were further investigated with regard to their role in virus life cycle. These two proteins are known to be involved in miRNA silencing and PKR regulation. Both interactions between NS1 and TRBP and NS1 and PACT were confirmed by co-immunoprecipitation, and both TRBP and PACT co-localized with NS1 in a cytosolic compartment. NS1 was also found to be present in the RISC complex in pull-down assays with the RISC core component Ago2. In functional assays, NS1 dose-dependently inhibited RNA silencing. Although no differences in TRBP-binding between NS1 proteins of various different influenza strains could be detected in direct mating Y2H assays, they varied with regard to their inhibitory activity on RNA silencing. TRBP and PACT alone were unable to restore NS1-induced inhibition of RNA silencing activity, however both together restored RNA silencing. Moreover, the siRNA knockdown of PACT abolished the association of NS1 with Ago2, and NS1 competitively inhibited the binding of TRBP and PACT to Ago2. The depletion of either TRBP or PACT led to an inhibition of influenza virus replication. The depletion of TRBP also lifted cellular IFNβ level without infection. However, the knockdown of TRBP but not PACT blocked IFNβ production and increased cell viability post infection. These results indicate that NS1 inhibits the binding of PACT and TRBP to the RISC complex and thereby inhibits miRNA-induced gene silencing. The hypothesis that TRBP supports influenza replication potentially by regulating PKR regulation and IFNβ induction requires further investigation. In conclusion, this study provides evidence for the complexity of virus-host interactions and the dual role of viral proteins in activating both positive and negative regulatory cellular mechanisms.

Influenza A virus (IAV) causes annual epidemics and sporadic pandemics of respiratory disease in humans. One of the main complications of primary IAV infection is increased susceptibility to secondary bacterial co-infection, with Staphylococcus aureus being the most common co-infecting species. Previous work identified secreted proteases from S. aureus as a pro-viral factor, leading to specific cleavage of the IAV surface hemagglutinin and increase in infectious viral titre. The aim of this study was to investigate the effect of bacterial proteases, and other secreted bacterial proteins, on IAV replication. Supernatants from the S. aureus community-associated epidemic clone USA300 were separated by size exclusion chromatography and each fraction was tested for an impact on IAV replication in primary chicken embryo fibroblast (CEF) cells. A fraction that increased viral titre by at least 10-fold was identified, but this effect was independent of known secreted proteases. Through the use of mass spectrometry fingerprinting and bacterial mutagenesis, a single protein, S. aureus lipase 1, was identified to be responsible for the pro-viral effect. Lipase 1 is expressed by an array of diverse S. aureus strains of distinct clonal origins. Both the native and recombinant form of lipase 1 were pro-viral only during the infection of primary cells, including primary human lung fibroblasts. Further validation of this interaction indicated lipase 1 was pro-viral in a concentration dependant manner and for a range of IAV strains. Investigation into the mechanism of action of lipase 1 revealed the protein acts during a single infectious cycle in a manner dependent on its active site. Time of addition studies and western blot analysis showed lipase 1 affects the later stages of virus replication, but there is no direct interaction with the virus particle; rather, the protein manipulates the cell, resulting in an increased number of infectious particles being produced. This work has identified and validated a single S. aureus protein, which affects IAV replication. Thus, it has elucidated some of the complex interactions that occur between the virus and bacteria during co-infection. It has also demonstrated a novel role for a bacterial enzyme in IAV replication, the study of which can further our understanding of both IAV and cell biology.

Lam, Ka Han. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 77-82). / Abstracts in English and Chinese. / Acknowledgement --- p.ii / Abstract --- p.iii / 摘要 --- p.v / Content --- p.vii / List of Abbreviations and Symbols --- p.xi / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Severity of influenza --- p.1 / Chapter 1.2 --- Introduction of influenza viruses --- p.3 / Chapter 1.2.1 --- Virion and genome structure --- p.4 / Chapter 1.2.2 --- The replication cycle of influenza viruses --- p.5 / Chapter 1.3 --- Influenza virus NP --- p.8 / Chapter 1.3.1 --- The importance of NP in RNP structure maintenance --- p.9 / Chapter 1.3.2 --- NP self oligomerization --- p.10 / Chapter 1.3.3 --- NP-RNA interaction --- p.12 / Chapter 1.3.4 --- NP and other interacting partners --- p.13 / Chapter 1.4 --- Aim of the project --- p.16 / Chapter Chapter 2 --- Materials and Methods / Chapter 2.1 --- Biological materials --- p.18 / Chapter 2.2 --- Construction of NP mutants --- p.19 / Chapter 2.3 --- Luciferase assay --- p.22 / Chapter 2.4 --- Western blot --- p.23 / Chapter 2.5 --- Protein expression and purification --- p.23 / Chapter 2.6 --- Circular dichroism spectroscopy --- p.24 / Chapter 2.7 --- Static Light scattering --- p.24 / Chapter 2.8 --- Surface plasmon resonance --- p.25 / Chapter 2.9 --- Co-immunoprecipitation (co-IP) --- p.26 / Chapter Chapter 3 --- Identification of residues crucial for NPB oligomerization and ribonucleoprotein activity / Chapter 3.1 --- Introduction --- p.27 / Chapter 3.2 --- Result --- p.31 / Chapter 3.2.1 --- NPB mutants showed deficiency in overall transcription and replication activity --- p.31 / Chapter 3.2.2 --- Expression and purification of NP mutants with low RNP activity --- p.37 / Chapter 3.2.2.1 --- Expression of MBP-tagged NP variants --- p.37 / Chapter 3.2.2.2 --- Purification of MBP-tagged NP variants --- p.38 / Chapter 3.2.3 --- Secondary structures of NP variants were comparable t o wild type NP --- p.41 / Chapter 3.2.4 --- NP variants with low RNP activity were abnormal in oligomerization in vitro --- p.42 / Chapter 3.2.5 --- NP variants with low RNP activity were impaired in homo-oligomer formation in vivo --- p.45 / Chapter 3.2.6 --- Discussion --- p.47 / Chapter Chapter 4 --- Identification of residues crucial for NP 一 RNA interaction and ribonucleoprotein activity / Chapter 4.1 --- Introduction --- p.56 / Chapter 4.2 --- Result --- p.58 / Chapter 4.2.1 --- NPB mutants showed deficiency in overall transcription and replication activity --- p.58 / Chapter 4.2.2 --- Expression and purification of NP variants with low RNP activity --- p.62 / Chapter 4.2.3 --- Secondary structures of NP variants were comparable t o wild type NP --- p.63 / Chapter 4.2.4 --- NP variants with low RNP activity were abnormal in RNA binding --- p.64 / Chapter 4.3 --- Discussion --- p.68 / Chapter Chapter 5 --- Conclusion and future prospect --- p.73 / Copyright --- p.76 / References --- p.77

The severe disease associated with seasonal epidemics of influenza A virus (IAV), as well as pandemic outbreaks, have highlighted the necessity for novel, broadly cross-reactive vaccination and therapeutic strategies against IAV. Our studies have focused on the contribution of IAV-specific CD8 T cells to mediating protection following IAV vaccination and infection as IAV-specific CD8 T cells are required for clearance of IAV. Further, IAV-specific CD8 T cells are typically cross-protective as they are generally directed at highly conserved areas of IAV. Recently, influenza virus-like particles (VLPs) have been developed from recombinant baculoviruses containing influenza proteins hemagglutinin (HA) and/or neuraminidase (NA) on the surface and matrix (M1) in the VLP core. Influenza VLPs induce potent antibody responses and have been shown to provide protection from morbidity and mortality during lethal homo- and hetero-subtypic IAV challenge. This suggests that conserved, VLP-induced CD8 T cell responses may also contribute to the overall protective ability of VLPs. However, whether influenza VLPs can induce influenza-specific CD8 T cell responses and if these T cells are protective during IAV challenge remains unknown. Here, I demonstrate that a single, intranasal vaccination with VLPs containing HA and M1 leads to a significant increase in HA533-specific CD8 T cells in the lungs and lung-draining lymph nodes. Our results also indicate that HA533-specific CD8 T cells primed by influenza VLP vaccination are significantly increased in the lungs following lethal IAV challenge. These VLP-induced memory CD8 T cells are critical in providing protection from lethality following subsequent challenge infections, as depletion of CD8 T cells leads to increased mortality, even when total, but not VLP-induced memory, CD8 T cell numbers have been allowed to recover prior to lethal dose IAV challenge. In addition, my studies also importantly demonstrate that these VLP-induced, HA533-specific CD8 T cells aid in protection from high-dose, heterosubtypic IAV infections where CD8 T cell epitopes are conserved, but the targets of neutralizing antibodies have been destroyed. This dissertation further elucidates the requirements for the regulation of the IAV-specific CD8 T cell response in the periphery (i.e. lung) by pDC and CD8α+ DC. Our studies have previously demonstrated that pDC or CD8α+ DC must present viral antigen in the context of MHC class I along with trans-presentation of IL-15 to effector, IAV-specific CD8 T cells in the lungs to protect the T cells from apoptosis and allow generation of the full magnitude CD8 T cell response needed to clear IAV infection. Herein, I demonstrate that in addition to antigen presentation and IL-15, costimulatory molecules on the surface of pDC and CD8α+ DC are also required. However, the specific costimulatory molecules required depends upon both the mouse strain utilized for IAV infection as well as DC subset. In addition to costimulatory molecules, I also demonstrate that the requirement for pDC and CD8α+ DC to be infected differs in order for them to participate in this pulmonary rescue of the IAV-specific CD8 T cell response. While CD8α+ DC are able to efficiently cross-present exogenous antigen, pDC must be directly infected and utilize the endogenous, direct antigen presentation pathway to present viral antigen to IAV-specific CD8 T cells in the lungs during IAV infection. These data suggest there are distinct differences between pDC and CD8α+ DC in their mechanism of regulating the pulmonary IAV-specific CD8 T cell response, which had not been previously appreciated. Together, the results presented herein further detail the mechanism of regulation of effector IAV-specific CD8 T cells by DC as well as the contribution of IAV-specific CD8 T cells to a novel, IAV VLP vaccination strategy. These findings highlight the importance of IAV-specific CD8 T cells in mediating protection following IAV vaccination and infection.

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

Mammalian Scribble is a target for proteins encoded by human papilloma virus, retro- and flaviviruses. Tick-borne encephalitis virus (TBEV) is a flavivirus that have evolved distinct strategies to escape antiviral responses. Information of how flaviviruses intrude on cell integrity comes from understanding of the roles that host-factors play when they interfere with viruses. The first part of this thesis describes a novel interaction between the TBEVNS5 protein and Scribble. The importance of the interaction was demonstrated by RNAi-mediated depletion of Scribble, which prevented suppression of JAK-STAT signaling by NS5. Together, these results define Scribble as a novel target for NS5. TBEV is known to cause central nervous system disease TBE in humans that can lead to cognitive dysfunction. A unifying theme in CNS related diseases are defects in neuronal extensions. We therefore addressed the effects of TBEV expression in PC12 cell differentiation, which is characterized by extensive neurite growth. Our data show that TBEVNS5 suppresses neurite outgrowth through the Rho GTPase Rac1. These findings provide evidence that Rac1 is an indirect target of NS5 in neurite inhibition. Scribble was recently implicated in spine morphogenesis. Thus, we tested the role of Scribble in neurite elongation. Depletion of Scribble in PC12 cells, reduced neurite density but increased length of those remaining. Moreover, Scribble bound components in the Ras/ERK cascade in a growth factor dependent manner. Together, these results demonstrate that Scribble controls neurite elongation by scaffolding MAPK components. Moreover, as loss of dendritic spines, actin-rich protrusions on neurons, is a feature in cognitive dysfunction we speculate that cognitive dysfunction in TBE might involve disturbed Scribble expression by NS5. We also investigated the binding between NS1 of Influenza A virus and Scribble. The PDZ domains of Scribble are usually selective for specific C-terminal motifs in proteins. Because NS1 has a canonical PDZ motif we tested if binding to Scribble depends on this motif. We found that Scribble binds NS1; the association is dependent on the NS1 C-terminus that is recognized by PDZ3-4 of Scribble. Together, these results suggest that Scribble is a target for the H5N1 NS1 protein / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: In press. Paper 3: Manuscript. Paper 4: Manuscript.

Los virus de influenza aviar de alta patogenicidad (IAAP) causan una enfermedad muy severa en pollos, los cuales frecuentemente inducen lesiones en el sistema nervioso central (SNC). Esta tesis recoge los resultados de tres estudios que se llevaron a cabo para determinar el mecanismo de patogénesis y neurotropismo, así como establecer la ruta de entrada al SNC para un virus H7N1 IAAP. En el primer estudio se estableció un modelo animal de infección en pollos libres de patógenos específicos, que consistía en la inoculación intranasal con el virus H7N1 IAAP. Para establecer este modelo, se utilizaron tres diferentes dosis del virus, obteniendo que las dosis más altas producen una enfermedad similar a la reportada para otros virus de IAAP. Además, se observó que las dosis más bajas causan infección demostrada porque con las dosis más bajas, el virus es hallado en muestras de tejido, muestras de heces y secreciones respiratorias. Adicionalmente, se pudo comprobar el alto neurotropismo del virus, ya que aún en pollos inoculados con bajas dosis el RNA viral es hallado en el CNS. La viremia fue detectada a un día post infección (dpi), sugiriendo que está podría ser la vía de diseminación al SNC. En el segundo estudio, se determinó la distribución topográfica del antígeno viral en el SNC durante las primeras horas post infección, lo cual permitió determinar que el virus se disemina de forma simétrica y bilateral en núcleos neurales del diencéfalo, mesencéfalo y rombencéfalo. La distribución del antígeno viral indica que el bulbo olfatorio y los nervios periféricos están involucrados en el proceso de invasión del SNC. El hallazgo de receptores aviares y humanos en las células endoteliales explica porque estas células son tan sensibles a la infección. El RNA viral fue hallado en el líquido cerebro espinal el primer dpi, lo que indica que el virus atraviesa la barrera hemato-encefálica (BHE). En el tercer estudio, la alteración de la BHE inducido por el virus H7N1 IAAP fue demostrado usando tres diferentes métodos que incluye la perfusión intracardial de Azul de Evans, la detección de la extravasación de la proteína del suero IgY, y evaluación del patrón de tinción con el marcador de las uniones fuertes de la BHE, ZO-1 y claudin-1. El antígeno viral fue observado a las 24 hpi en las células endoteliales, mientras que el daño de la BHE fue observado a las 36 hpi y 48 hpi. En resumen, se puede afirmar que el virus H7N1 IAAP se disemina por la vía hematógena durante las primeras horas pi, posiblemente favorecido por la presencia de receptores en las células endoteliales del sistema nervioso central, y poco después daña la BHE durante las primeras horas de infección como se demuestra por la presencia de extravasación del azul de Evans and IgY del suero. / Highly pathogenic avian influenza viruses (HPAIV) cause a very severe systemic disease in chickens, in which is also frequent to find central nervous system (CNS) lesions. In this thesis, three studies were undertaken in order to determine the mechanism of pathogenesis, the neurotropism and establish the route of entry into the CNS use for a H7N1 HPAI virus. In the first study, an animal model was set up that consisted of SPF chickens inoculated intranasally with the H7N1 HPAI virus. To do that, three different doses were used, obtaining that the highest dose induced a disease similar to the produce by other HPAI viruses, moreover, it was also observed that very low doses also cause infection demonstrated because viral RNA was found in tissues samples, faeces and respiratory secretions. Besides, the high neurotropism of this virus was demonstrated because still in chickens inoculated with low doses, viral RNA is found in the brain. Viremia was detected at one dpi, which indicated that the bloodstream is the pathway of viral spreading to the brain. In the second study, the topographical distribution study of the viral antigen during the first dpi was determined, which allow to determine that the virus disseminates showing a symmetrical and bilateral pattern in the diencephalon, mesencephalon and rhombencephalon, whereas in the telencephalon and cerebellum it was multifocal and random. Viral antigen distribution indicates that the olfactory bulb (OB) and peripheral nerves are not involved in the process of virus invasion into the brain. Avian and human influenza receptors were found in endothelial cells which explain why these cells are so sensitive to the infection. Viral RNA was found in cerebrospinal fluid (CSF) at one dpi, indicating that the virus was able to cross blood brain barrier (BBB). In the third study, the disruption of the BBB induce by the H7N1 HPAI was demonstrated using three different methods that include the intracardial perfusion of the tracer Evans blue (EB), detection of the extravasation serum IgY, and evaluation of the pattern of staining of the tight junction proteins ZO-1 and claudin-1. Viral antigen can be observed as early as 24 hpi in the endothelial cells, whereas disruption was detected at 36 and 48 hpi. In summary, it can be asserted that this H7N1 HPAIV disseminates via the haematogenous route early during the infection, favored by the presence of abundant receptors on the CNS endothelial cells, and soon after it disrupts the BBB during the first hours of infection as demonstrated by the presence of EB and serum IgY extravasation.

published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

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